How to set the default fill type to NOTHING (Cone, Cylinder), once and for all?
You can see the property names by hovering mouse above the field. 



Note that you need to match this name in the first part of the script file before the =. The latter needs to define property in blender operator format. For the dropdown menu it's in fact enumerator type, not string. You can't really specify default value for enumerator but I found that this has the desired effect nonetheless. So the file should look like this (note you need to import EnumProperty in the beginning as well):

from bpy.props import IntProperty
from bpy.props import EnumProperty
from bpy.types import (
    MESH_OT_primitive_circle_add,
    MESH_OT_primitive_cone_add,
    MESH_OT_primitive_cylinder_add,
    MESH_OT_primitive_uv_sphere_add,
)

MESH_OT_primitive_circle_add.vertices = IntProperty(name="Vertices", default=12)
MESH_OT_primitive_circle_add.fill_type = EnumProperty(items=[('NOTHING', 'Nothing', 'Tooltip'), ('NGON', 'Ngon', 'Tooltip'), ('TRIFAN', 'Triangle Fan', 'Tooltip')], name="Fill Type")
MESH_OT_primitive_cone_add.end_fill_type = EnumProperty(items=[('NOTHING', 'Nothing', 'Tooltip'), ('NGON', 'Ngon', 'Tooltip'), ('TRIFAN', 'Triangle Fan', 'Tooltip')], name="Fill Type")
MESH_OT_primitive_cylinder_add.end_fill_type = EnumProperty(items=[('NOTHING', 'Nothing', 'Tooltip'), ('NGON', 'Ngon', 'Tooltip'), ('TRIFAN', 'Triangle Fan', 'Tooltip')], name="Fill Type")
MESH_OT_primitive_cone_add.vertices = IntProperty(name="Vertices", default=12)
MESH_OT_primitive_cylinder_add.vertices = IntProperty(name="Vertices", default=12)


If you need to create certain type of geometry often you might as well copy the operator that creates it and store it in script file or python console where you can execute it. You can store all the properties you can edit in the side panel.



Drag the top info bar down and right click to select and CTRL-C to copy the lines for quickly using them later. You can even make them their own operators, add them to menus or add keybinds to them.